I have submitted a new Mesh Baker update to the asset store. The update includes a number of enhancements.
Better support for the Unity 5 Standard Shader
If a texture slot is blank in a material Mesh Baker will now try to find the appropriate color property and use that instead of using a black color in the atlas.
More efficient scene analysis and validation.
Mesh validation checks are now cached. This improves speed if many objects use the same sharedMesh.
New Filter For Objects That Have Already Been Added To A Baker
In a complicated scene it can be difficult to ensure that objects are not accidentally added to two different bakers and baked into the scene twice. A new filter is now available to exclude objects that have already been added to a baker.
The update also includes a few other minor bug fixes